Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003307.1 Kokia drynarioides strain JFW-HI SEQ_115992, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 83072
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:1008 original size:6 final size:6
Alignment explanation
Indices: 990--1067 Score: 69
Period size: 6 Copynumber: 14.0 Consensus size: 6
980 TGAGATTTAT
* * * *
990 TTTAAA TTCAAA TTTAAA -TCAAG TTTAAA TTT-AT TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
1036 -TT-AA TTTGAA TTTAAA TTT--A TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
1068 ATAAATAAAT
Statistics
Matches: 57, Mismatches: 9, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
4 6 0.11
5 11 0.19
6 40 0.70
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (6 bp):
TTTAAA
Found at i:1027 original size:11 final size:11
Alignment explanation
Indices: 984--1066 Score: 73
Period size: 11 Copynumber: 7.5 Consensus size: 11
974 CCATTTTGAG
*
984 ATTTATTTTAA
1 ATTTAATTTAA
*
995 ATTCAAATTTAA
1 ATT-TAATTTAA
*
1007 A-TCAAGTTTAA
1 ATTTAA-TTTAA
*
1018 ATTTATTTTAA
1 ATTTAATTTAA
*
1029 ATTTAAATT-A
1 ATTTAATTTAA
1039 ATTTGAATTTAA
1 ATTT-AATTTAA
1051 ATTT-ATTTAA
1 ATTTAATTTAA
1061 ATTTAA
1 ATTTAA
1067 AATAAATAAA
Statistics
Matches: 58, Mismatches: 8, Indels: 12
0.74 0.10 0.15
Matches are distributed among these distances:
10 17 0.29
11 27 0.47
12 14 0.24
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (11 bp):
ATTTAATTTAA
Found at i:1033 original size:17 final size:17
Alignment explanation
Indices: 984--1067 Score: 91
Period size: 17 Copynumber: 5.1 Consensus size: 17
974 CCATTTTGAG
* *
984 ATTTATTTTAAATTCAA
1 ATTTAATTTAAATTTAA
* * *
1001 ATTTAAATCAAGTTTAA
1 ATTTAATTTAAATTTAA
*
1018 ATTTATTTTAAATTTAA
1 ATTTAATTTAAATTTAA
*
1035 A-TTAATTTGAATTTAA
1 ATTTAATTTAAATTTAA
1051 ATTT-ATTTAAATTTAA
1 ATTTAATTTAAATTTAA
1067 A
1 A
1068 ATAAATAAAT
Statistics
Matches: 54, Mismatches: 12, Indels: 3
0.78 0.17 0.04
Matches are distributed among these distances:
16 26 0.48
17 28 0.52
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (17 bp):
ATTTAATTTAAATTTAA
Found at i:1049 original size:16 final size:16
Alignment explanation
Indices: 990--1067 Score: 75
Period size: 16 Copynumber: 4.8 Consensus size: 16
980 TGAGATTTAT
*
990 TTTAAATTCAAATTTAA
1 TTTAAATTTAAA-TTAA
* * * *
1007 ATCAAGTTTAAATTTAT
1 TTTAAATTTAAA-TTAA
1024 TTTAAATTTAAATTAA
1 TTTAAATTTAAATTAA
* *
1040 TTTGAATTTAAATTTA
1 TTTAAATTTAAATTAA
1056 TTTAAATTTAAA
1 TTTAAATTTAAA
1068 ATAAATAAAT
Statistics
Matches: 49, Mismatches: 12, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
16 28 0.57
17 21 0.43
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (16 bp):
TTTAAATTTAAATTAA
Found at i:1728 original size:17 final size:16
Alignment explanation
Indices: 1704--1735 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
1694 AATAATAACA
1704 TTAATATAATAAATAT
1 TTAATATAATAAATAT
1720 TTAATTATAATAAATA
1 TTAA-TATAATAAATA
1736 AAAAAGAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
TTAATATAATAAATAT
Found at i:2830 original size:30 final size:29
Alignment explanation
Indices: 2796--2864 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 29
2786 CCCAGAAGGA
* *
2796 CCTTAAACTATCCAAAAATCATATTTTGAC
1 CCTTAAACTATCC-AAAATCACATTTTAAC
* *
2826 CCTTACACTTTTCCAAAATCACATTTTAAC
1 CCTTAAAC-TATCCAAAATCACATTTTAAC
*
2856 CCTCAAACT
1 CCTTAAACT
2865 TCTTAAAATT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
29 1 0.03
30 27 0.84
31 4 0.12
ACGTcount: A:0.36, C:0.29, G:0.01, T:0.33
Consensus pattern (29 bp):
CCTTAAACTATCCAAAATCACATTTTAAC
Found at i:2973 original size:29 final size:29
Alignment explanation
Indices: 2799--3152 Score: 176
Period size: 29 Copynumber: 12.2 Consensus size: 29
2789 AGAAGGACCT
* * * * *
2799 TAAACTATCCAAAAATCATATTTTGACCC
1 TAAACTTTTCAAAAATTACATTTTTACCC
* * * *
2828 TTACACTTTTCCAAAATCACATTTTAACCC
1 -TAAACTTTTCAAAAATTACATTTTTACCC
*
2858 TCAAACTTCTT-AAAATTTAC-TTTTT-CCC
1 T-AAACTT-TTCAAAAATTACATTTTTACCC
* * *
2886 CAAAC-TTCCAAAAATTACAATTTTACCCC
1 TAAACTTTTCAAAAATTACATTTTTA-CCC
** *
2915 CGAACTTTTCAAAAA-TACATGTTTACCCC
1 TAAACTTTTCAAAAATTACATTTTTA-CCC
2944 TAAACTTTTCAAAAATTACATTTTTACCC
1 TAAACTTTTCAAAAATTACATTTTTACCC
* * **
2973 TTAA-TCTTCCAAAAATTACATATTTGCCCC
1 TAAACT-TTTCAAAAATTACAT-TTTTACCC
*
3003 TAAA-TTTCTTAAAAATTACATTTTT-CTCC
1 TAAACTTT-TCAAAAATTACATTTTTAC-CC
* * * *
3032 TGAACTTCT-AAAAATCACATTTTTTCCC
1 TAAACTTTTCAAAAATTACATTTTTACCC
* * ** *
3060 TCAAAC-TTCCAAAAATCATGTTTTTTCCC
1 T-AAACTTTTCAAAAATTACATTTTTACCC
* *
3089 -AAA-TTTTCCCAAAATGACATTTTTACCCC
1 TAAACTTTT-CAAAAATTACATTTTTA-CCC
* * *
3118 TAAAAC-TTTCCAAAATTGCATTTTAACCC
1 T-AAACTTTTCAAAAATTACATTTTTACCC
*
3147 CAAACT
1 TAAACT
3153 CTCCGAAACT
Statistics
Matches: 253, Mismatches: 48, Indels: 47
0.73 0.14 0.14
Matches are distributed among these distances:
25 1 0.00
26 9 0.04
27 13 0.05
28 39 0.15
29 95 0.38
30 88 0.35
31 8 0.03
ACGTcount: A:0.35, C:0.26, G:0.02, T:0.37
Consensus pattern (29 bp):
TAAACTTTTCAAAAATTACATTTTTACCC
Found at i:3587 original size:97 final size:97
Alignment explanation
Indices: 3421--3610 Score: 299
Period size: 97 Copynumber: 2.0 Consensus size: 97
3411 AAAATATTTA
* *
3421 AAATCAAGGTAATATTCCTTTATTTCGGATTTTGAAAATTCGTGCCTTAACTTACTAGGCGCGAT
1 AAATCAAGGCAATATTCCTTTATTTCGGATTTTGAAAATTCGTGCCTTAACTTACTAGGCGCGAC
*
3486 TTTTCTTCAAATCGGGATAATCAAATACCCTT
66 TTTTCTTCAAATCGAGATAATCAAATACCCTT
* * * *
3518 AAATCGAGGCAATATTCTTTTATTTCGGGTTTTGAAAATTTGTGCCTTAACTTACTAGGCGCGAC
1 AAATCAAGGCAATATTCCTTTATTTCGGATTTTGAAAATTCGTGCCTTAACTTACTAGGCGCGAC
* *
3583 TTTTCTTTAAATCGAGATAATCGAATAC
66 TTTTCTTCAAATCGAGATAATCAAATAC
3611 TCTTTTTCAA
Statistics
Matches: 84, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
97 84 1.00
ACGTcount: A:0.29, C:0.17, G:0.16, T:0.37
Consensus pattern (97 bp):
AAATCAAGGCAATATTCCTTTATTTCGGATTTTGAAAATTCGTGCCTTAACTTACTAGGCGCGAC
TTTTCTTCAAATCGAGATAATCAAATACCCTT
Found at i:5159 original size:22 final size:22
Alignment explanation
Indices: 5134--5196 Score: 68
Period size: 18 Copynumber: 3.2 Consensus size: 22
5124 CAGATAATTA
5134 AATTTCTAATAAAAAACTATAT
1 AATTTCTAATAAAAAACTATAT
*
5156 AA--T-TAA-AAATAA-T-T-T
1 AATTTCTAATAAAAAACTATAT
5171 AATTTCTAATAAAAAACTATAT
1 AATTTCTAATAAAAAACTATAT
5193 AATT
1 AATT
5197 AAAAAAAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 14
0.67 0.04 0.29
Matches are distributed among these distances:
15 3 0.09
16 1 0.03
17 2 0.06
18 8 0.25
19 8 0.25
20 2 0.06
21 1 0.03
22 7 0.22
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (22 bp):
AATTTCTAATAAAAAACTATAT
Found at i:5169 original size:37 final size:37
Alignment explanation
Indices: 5127--5201 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
5117 TTAAATTCAG
5127 ATAATTAAATTTCTAATAAAAAACTATATAATTAAAA
1 ATAATTAAATTTCTAATAAAAAACTATATAATTAAAA
*
5164 ATAATTTAATTTCTAATAAAAAACTATATAATTAAAA
1 ATAATTAAATTTCTAATAAAAAACTATATAATTAAAA
5201 A
1 A
5202 AAATAGTCAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (37 bp):
ATAATTAAATTTCTAATAAAAAACTATATAATTAAAA
Found at i:7210 original size:22 final size:23
Alignment explanation
Indices: 7184--7227 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
7174 TTTTAAAACA
7184 AATATTT-AT-ATTGTTTTATTTT
1 AATATTTAATAATT-TTTTATTTT
7206 AATATTTAATAATTTTTTATTT
1 AATATTTAATAATTTTTTATTT
7228 ATTGAAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 7 0.35
23 10 0.50
24 3 0.15
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (23 bp):
AATATTTAATAATTTTTTATTTT
Found at i:7596 original size:16 final size:16
Alignment explanation
Indices: 7575--7606 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
7565 CATCTCTTAT
7575 TCTTATTCCAAATCGA
1 TCTTATTCCAAATCGA
*
7591 TCTTATTCCATATCGA
1 TCTTATTCCAAATCGA
7607 ATCGAATTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.28, C:0.25, G:0.06, T:0.41
Consensus pattern (16 bp):
TCTTATTCCAAATCGA
Found at i:8476 original size:13 final size:13
Alignment explanation
Indices: 8458--8484 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
8448 AATTGAATTT
8458 AAAGAAAAAAAAG
1 AAAGAAAAAAAAG
8471 AAAGAAAAAAAAG
1 AAAGAAAAAAAAG
8484 A
1 A
8485 GAGTGTCCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (13 bp):
AAAGAAAAAAAAG
Found at i:8590 original size:21 final size:21
Alignment explanation
Indices: 8566--8606 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
8556 CTCAGTCAAC
8566 AAAAGACCAAAA-ATAAACCCA
1 AAAAG-CCAAAACATAAACCCA
*
8587 AAAAGCCAAAACCTAAACCC
1 AAAAGCCAAAACATAAACCC
8607 CCCATAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.61, C:0.29, G:0.05, T:0.05
Consensus pattern (21 bp):
AAAAGCCAAAACATAAACCCA
Found at i:20565 original size:21 final size:21
Alignment explanation
Indices: 20524--20568 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
20514 GATATACGGA
*
20524 ACTAACAGTGAGTACTGAAGT
1 ACTAACAGTGAGCACTGAAGT
*
20545 ACTATCAGTGAGCACAT-AAGT
1 ACTAACAGTGAGCAC-TGAAGT
20566 ACT
1 ACT
20569 GAGAAAACAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 20 0.95
22 1 0.05
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.24
Consensus pattern (21 bp):
ACTAACAGTGAGCACTGAAGT
Found at i:20608 original size:23 final size:23
Alignment explanation
Indices: 20572--20675 Score: 145
Period size: 23 Copynumber: 4.5 Consensus size: 23
20562 AAGTACTGAG
* *
20572 AAAACAGTAAGCACACACAGTGT
1 AAAACAATAAGCACACACAGTGC
*
20595 AAAACAATAGGCACACACAGTGC
1 AAAACAATAAGCACACACAGTGC
20618 AAAACAATAAGCACACACAGTGC
1 AAAACAATAAGCACACACAGTGC
* *
20641 AAATCAGTAAGCACACACAGTGC
1 AAAACAATAAGCACACACAGTGC
**
20664 TGAACAATAAGC
1 AAAACAATAAGC
20676 GTGCTAATGT
Statistics
Matches: 71, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 71 1.00
ACGTcount: A:0.48, C:0.24, G:0.16, T:0.12
Consensus pattern (23 bp):
AAAACAATAAGCACACACAGTGC
Found at i:20828 original size:2 final size:2
Alignment explanation
Indices: 20821--20848 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
20811 ATGTCTATTT
20821 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
20849 TACATACATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:23658 original size:150 final size:150
Alignment explanation
Indices: 23431--23726 Score: 513
Period size: 150 Copynumber: 2.0 Consensus size: 150
23421 CACATTAAAT
23431 CATAGTTCATGTATATTTTTGAGATTTATCTAAAAAAATTACTATTTATCTTTTGAAATACTACT
1 CATAGTTCATGTATATTTTTGAGATTTATCTAAAAAAATTACTATTTATCTTTTGAAATACTACT
* * *
23496 ATACATGAACTTTTGGTATTATCGTGCTTAGGAGGATTCGAAAAATTTTGAGAGCTGAAGGGAAA
66 ATACATGAACTTTTGATATTATCGTGCTTAGGAGGATTCGAAAAATTTTGAGAGATGAAAGGAAA
23561 TGGTACATTAGACATGCATA
131 TGGTACATTAGACATGCATA
* * *
23581 CATAGTTCATGTATATTTTTTG-GATTTATCTAAAAAATTTATTTTTTATCTTTTGAAATACTAC
1 CATAGTTCATGTATA-TTTTTGAGATTTATCTAAAAAAATTACTATTTATCTTTTGAAATACTAC
*
23645 TATACATGAACTTTTGATATTATCGTGCTTAGGAGGATTCGAAAATTTTTGAGAGATGAAAGGAA
65 TATACATGAACTTTTGATATTATCGTGCTTAGGAGGATTCGAAAAATTTTGAGAGATGAAAGGAA
23710 ATGGTACATTAGACATG
130 ATGGTACATTAGACATG
23727 TATATAGAGA
Statistics
Matches: 138, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
150 132 0.96
151 6 0.04
ACGTcount: A:0.34, C:0.10, G:0.17, T:0.39
Consensus pattern (150 bp):
CATAGTTCATGTATATTTTTGAGATTTATCTAAAAAAATTACTATTTATCTTTTGAAATACTACT
ATACATGAACTTTTGATATTATCGTGCTTAGGAGGATTCGAAAAATTTTGAGAGATGAAAGGAAA
TGGTACATTAGACATGCATA
Found at i:35331 original size:20 final size:20
Alignment explanation
Indices: 35306--35343 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
35296 TCTACAAAAA
*
35306 AAATCTCTAAGATTACAATC
1 AAATCTCTAAGATCACAATC
35326 AAATCTCTAAGATCACAA
1 AAATCTCTAAGATCACAA
35344 GGATCATATC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.21, G:0.05, T:0.26
Consensus pattern (20 bp):
AAATCTCTAAGATCACAATC
Found at i:39511 original size:18 final size:17
Alignment explanation
Indices: 39470--39513 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
39460 TGAATAAAAA
*
39470 ATTGATTG-AAGTTTTG
1 ATTGATTGAAAGTTTAG
39486 ATTCGATTGAAAGTGTTAG
1 ATT-GATTGAAAGT-TTAG
39505 ATTGATTGA
1 ATTGATTGA
39514 TTTGCAATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 3 0.12
17 5 0.21
18 10 0.42
19 6 0.25
ACGTcount: A:0.30, C:0.02, G:0.25, T:0.43
Consensus pattern (17 bp):
ATTGATTGAAAGTTTAG
Found at i:46314 original size:7 final size:7
Alignment explanation
Indices: 46302--46335 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
46292 TAAGCCTTAC
46302 TTCTTTT
1 TTCTTTT
46309 TTCTTTT
1 TTCTTTT
46316 TTCTTTT
1 TTCTTTT
*
46323 TTTTTCTT
1 TTCTT-TT
46331 TTCTT
1 TTCTT
46336 CTAAATTTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
7 18 0.75
8 6 0.25
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (7 bp):
TTCTTTT
Found at i:55287 original size:20 final size:18
Alignment explanation
Indices: 55248--55283 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
55238 CCACCAAAAA
55248 TAAAATATATATTTAAAT
1 TAAAATATATATTTAAAT
*
55266 TAAACTATATATTTAAAT
1 TAAAATATATATTTAAAT
55284 ATTATATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (18 bp):
TAAAATATATATTTAAAT
Found at i:56329 original size:27 final size:27
Alignment explanation
Indices: 56275--56330 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 27
56265 TTTATTTTAA
* * *
56275 TATTTAATATTTTTATACATTTTTATT
1 TATTGAATATTTTTATACATATTCATT
* *
56302 TATTGAATTTTTTTATATATATTCATT
1 TATTGAATATTTTTATACATATTCATT
56329 TA
1 TA
56331 ACATTATTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.64
Consensus pattern (27 bp):
TATTGAATATTTTTATACATATTCATT
Found at i:67994 original size:31 final size:29
Alignment explanation
Indices: 67957--68023 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 29
67947 ATCTCAAAAT
* *
67957 TATACATCAACTATGGTTTAATGTGCAATTA
1 TATACATAAACTATGATTT--TGTGCAATTA
* *
67988 TATACATAAACTTTGATTTTGTGCAATTT
1 TATACATAAACTATGATTTTGTGCAATTA
68017 TATACAT
1 TATACAT
68024 TATTTTATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 16 0.50
31 16 0.50
ACGTcount: A:0.34, C:0.12, G:0.10, T:0.43
Consensus pattern (29 bp):
TATACATAAACTATGATTTTGTGCAATTA
Found at i:71890 original size:21 final size:21
Alignment explanation
Indices: 71854--71919 Score: 75
Period size: 19 Copynumber: 3.1 Consensus size: 21
71844 TTTCGTGCTG
71854 TTTTGATTGATTTTTTTTACTAT
1 TTTTGA-TG-TTTTTTTTACTAT
*
71877 TTTTG-TG-TTTTTTTACT-G
1 TTTTGATGTTTTTTTTACTAT
71895 TTTTGATGCTTTTTTTTACTAT
1 TTTTGATG-TTTTTTTTACTAT
71917 TTT
1 TTT
71920 GGTTGTTATT
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
18 5 0.14
19 12 0.32
21 12 0.32
22 3 0.08
23 5 0.14
ACGTcount: A:0.12, C:0.06, G:0.11, T:0.71
Consensus pattern (21 bp):
TTTTGATGTTTTTTTTACTAT
Found at i:71920 original size:21 final size:20
Alignment explanation
Indices: 71854--71920 Score: 75
Period size: 21 Copynumber: 3.2 Consensus size: 20
71844 TTTCGTGCTG
71854 TTTTGATTGATTTTTTTTACTA
1 TTTTGA-TG-TTTTTTTTACTA
*
71876 TTTT--TGTGTTTTTTTACTG
1 TTTTGATGT-TTTTTTTACTA
71895 TTTTGATGCTTTTTTTTACTA
1 TTTTGATG-TTTTTTTTACTA
71916 TTTTG
1 TTTTG
71921 GTTGTTATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
18 1 0.03
19 16 0.41
21 17 0.44
22 5 0.13
ACGTcount: A:0.12, C:0.06, G:0.12, T:0.70
Consensus pattern (20 bp):
TTTTGATGTTTTTTTTACTA
Found at i:71929 original size:12 final size:12
Alignment explanation
Indices: 71914--72029 Score: 81
Period size: 12 Copynumber: 9.1 Consensus size: 12
71904 TTTTTTTTAC
*
71914 TATTTTGGTTGT
1 TATTTTTGTTGT
*
71926 TATTTTCG-TGT
1 TATTTTTGTTGT
*
71937 TGTTTTTGTTGT
1 TATTTTTGTTGT
*
71949 TATTTTTGTTGC
1 TATTTTTGTTGT
71961 TATTTTTGTTGTTTT
1 TATTTTTGTTG---T
*
71976 TAATTTTGCTTGCTGT
1 T-A-TTT--TTGTTGT
* *
71992 TATTTTTTGCTGC
1 TA-TTTTTGTTGT
*
72005 TATTTTGGTTGT
1 TATTTTTGTTGT
72017 TATTTTTGTTGT
1 TATTTTTGTTGT
72029 T
1 T
72030 TGGATGTTAT
Statistics
Matches: 84, Mismatches: 12, Indels: 16
0.75 0.11 0.14
Matches are distributed among these distances:
11 9 0.11
12 50 0.60
13 8 0.10
15 6 0.07
16 3 0.04
17 3 0.04
19 5 0.06
ACGTcount: A:0.08, C:0.05, G:0.19, T:0.68
Consensus pattern (12 bp):
TATTTTTGTTGT
Found at i:72043 original size:44 final size:43
Alignment explanation
Indices: 71913--72043 Score: 131
Period size: 44 Copynumber: 2.9 Consensus size: 43
71903 CTTTTTTTTA
* *
71913 CTATTTTGGTTGTTATTTTCGTGTTGTTTTTGTTGTTATTTTTGTTG
1 CTATTTTGGTTGTTATTTT--TGTTG--TTTGATGTTATTTTTGCTG
* * *
71960 CTATTTTTGTTGTT-TTTAATT-TTGCTTGCTGTTATTTTTTGCTG
1 CTATTTTGGTTGTTATTT--TTGTTGTTTGATGTTA-TTTTTGCTG
72004 CTATTTTGGTTGTTATTTTTGTTGTTTGGATGTTATTTTT
1 CTATTTTGGTTGTTATTTTTGTTGTTT-GATGTTATTTTT
72044 ATGCGTTTTT
Statistics
Matches: 71, Mismatches: 7, Indels: 15
0.76 0.08 0.16
Matches are distributed among these distances:
43 10 0.14
44 31 0.44
45 12 0.17
46 4 0.06
47 13 0.18
48 1 0.01
ACGTcount: A:0.08, C:0.05, G:0.19, T:0.67
Consensus pattern (43 bp):
CTATTTTGGTTGTTATTTTTGTTGTTTGATGTTATTTTTGCTG
Found at i:75561 original size:24 final size:24
Alignment explanation
Indices: 75515--75568 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
75505 GAGCCTGAAT
**
75515 CTGAGCATGAGCTCAGTCCCGAGC
1 CTGAGCATGAGCTCAAACCCGAGC
75539 CTGAGCATGAGC-CAAACCTCGAGC
1 CTGAGCATGAGCTCAAACC-CGAGC
*
75563 CCGAGC
1 CTGAGC
75569 CAACCCCTGA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 4 0.15
24 22 0.85
ACGTcount: A:0.24, C:0.35, G:0.28, T:0.13
Consensus pattern (24 bp):
CTGAGCATGAGCTCAAACCCGAGC
Found at i:82438 original size:13 final size:13
Alignment explanation
Indices: 82422--82456 Score: 56
Period size: 11 Copynumber: 2.8 Consensus size: 13
82412 AGGTTTTTTT
82422 CAAAAAAATACGA
1 CAAAAAAATACGA
82435 C--AAAAATACGA
1 CAAAAAAATACGA
82446 CAAAAAAATAC
1 CAAAAAAATAC
82457 CTGACATCCA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
11 11 0.55
13 9 0.45
ACGTcount: A:0.69, C:0.17, G:0.06, T:0.09
Consensus pattern (13 bp):
CAAAAAAATACGA
Found at i:82706 original size:11 final size:11
Alignment explanation
Indices: 82690--82735 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
82680 GGGGACCAAC
* *
82690 GAAAAATGAAG
1 GAAAAAAGAAA
82701 GAAAAAAGAAA
1 GAAAAAAGAAA
82712 GAAAAAAG--A
1 GAAAAAAGAAA
82721 GAAAGAAAGAAA
1 GAAA-AAAGAAA
82733 GAA
1 GAA
82736 GGAAGAGGAG
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
9 5 0.17
10 4 0.13
11 17 0.57
12 4 0.13
ACGTcount: A:0.74, C:0.00, G:0.24, T:0.02
Consensus pattern (11 bp):
GAAAAAAGAAA
Found at i:82741 original size:21 final size:20
Alignment explanation
Indices: 82697--82742 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 20
82687 AACGAAAAAT
82697 GAAG-GAAAAAAGAAAGAAA
1 GAAGAGAAAAAAGAAAGAAA
* *
82716 AAAGAGAAAGAAAGAAAGAAG
1 GAAGAGAAA-AAAGAAAGAAA
82737 GAAGAG
1 GAAGAG
82743 GAGAAGAAGG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 3 0.14
20 4 0.18
21 15 0.68
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (20 bp):
GAAGAGAAAAAAGAAAGAAA
Done.